I hope so. I makes total sense. In Avengers 1 Fury talks about how they were using Hydra weapons to build something because suddenly Thor, Loki, and the Hulk were showing up and seen as major possible threats. So now, after Loki and the alien invasion, it makes total sense that Fury would create a section of SHIELD that would deal exclusively with alien threats. And I think they would, and should, play a huge role in the Captain Marvel/Carol Danvers movie.